This page gives pointers to
These are freely-available molecular dynamics codes, most of them parallel, which may be well-suited to the problems you want to model. They can be used in conjunction with LAMMPS to perform complementary modeling tasks.
CHARMM, AMBER, GROMACS, NAMD, NWCHEM, and Tinker are designed primarily for modeling biological molecules. CHARMM and AMBER are the original classic codes in this genre. Gromacs and NAMD and NWCHEM are more recently developed codes. Tinker is a serial code.
DL_POLY includes potentials for a variety of biological and non-biological materials. HOOMD is a very fast MD code designed to run on GPUs.